The Unknown
by Lordoftheghostking28
Summary: When the Enterprise stumbles upon a Klingon vessel dead in space, they get a nasty surprise: All the Klingons aboard are dead. Except for one...now they have to find the survivor; before a strange group of aliens do.
1. Chapter 1

"Full speed ahead, Mr. Sulu," Captain James T. Kirk said, a small smile playing on his lips.

"Full speed ahead, sir," Hikaru Sulu said, adjusting a few knobs on the control panel in front of him. The _Enterprise_ and her crew were off to another uncharted part of the galaxy, scheduled for photographing the sector and finding planets suitable for life.

The only thing that could go wrong, in Kirk's eyes, would be if the engines gave out.

He smiled to himself, picturing his top engineer, Scotty, saying, 'I need more, time, sir. I dinna think that this here kit n' caboodle was as badly damaged as it was.' This had happened on more than one occasion.

"Captain, we should be reaching the uncharted sector in 4.29 minuets if we stay at this current speed."

Kirk turned to see his Science Officer, Spock, standing beside him. Spock cocked a slanted eyebrow. "Is something the matter, Captain?"

"No, Spock, just thinking." Kirk sighed. "I wonder if we'll find anything worth investigating out here."

"If my suspicions are correct, Captain, then we will."

"Really? Like what? What could be living out here in deep space?"

"Time will only answer your questions, Captain,"

**XxXxXxXx**

Meanwhile, further in the star sector, just off of the Enterprises' scanners, a Klingon ship hovered in space. Aboard the ship, many crew members lay dead, killed by some sort of alien…

The Klingon captain, Korr, had his back pressed against his quarter's doors, keeping it from opening to the aliens. He pressed a small nearby button, saying clearly, "If anyone…anyone at all…can hear my message, get somewhere safe. These things can't be killed like other life forms. Our best strategy is to take shelter and wait."

A loud screech came from behind the closed quarter's doors, chilling Korr to the bone. He knew his crew was dead and he knew the mysterious aliens would find a way into the doors eventually.

Then why did he delay his death? He wished he knew.

**XxXxXxXx**

As impossible as it was, Samus Aran knew it was true. Metroids had taken refuge on a spacecraft and were probably now feasting on the inhabitants' power. Just how they had managed to get onto the ship, she had no idea. She would have to locate survivors and question them…if there still were any survivors.

She pulled her spacecraft up to the side of what looked to be a striking resemblance to a predatory bird. "Bird of prey." She thought, locking her ship over an emergency evacuation hatch. A few blasts with her ice beam and she had an entrance. She climbed into the ship and looked around, activating her Power Suit as she did so.

You could never be too careful around Metroids. She began making her way down the hall. A body lay near a door, covered in something that confirmed Samus' worst fears. Metroids were aboard. She quickened her pace, finding a map of the ship. Locating the bridge, she set out.

**XxXxXxXx**

"Checkmate," Kirk smiled.

Spock took a few seconds to observe the board, finally saying, "I regret to admit that you are correct, captain."

Kirk snickered. "You are a worthy opponent, Spock."

"Thank you, Captain. I must say-" Spock was cut off by a sharp whistle of an incoming message from the bridge.

"Captain, we're approaching a spacecraft. All hailing frequencies are open, but they are not responding." Lieutenant Uhura informed. "Sulu thinks its Klingons."

"I'll be right there." Kirk quickly left the recreational room, Spock close behind.

They stepped into an elevator and sped upwards towards the bridge, nearly running into the chief engineer as they stepped hurriedly out.

"Sorry, sir." Scott muttered.

"It's fine, Scotty." Kirk headed for the command chair. "Do we have visual?"

"Yes, sir, we just came within range." Uhura said.

"On screen."

The gray-green color of the Klingon bird-of-prey warship swam into view in the darkness of space. It was just sitting there, as though it had lost all power. "Open a channel, Lieutenant." Kirk said.

Uhura flicked a few switches and said, "Go ahead, captain. Channels open."

"This is the USS Enterprise. I'm Captain Kirk. Please state your business in this sector."

Silence greeted him.

"Captain, there appears to be a small orange craft of some kind on the lift side of the cruiser," Spock said, examining the image at the science station. "I'm beginning to suspect they've been ambushed."

"An entire crew of Klingons overrun by the crew of that ship?" Kirk sighed. "That is very well a possibility. Uhura, open a channel directly to their bridge. I want visual as well."

The visual came. Kirk stood in shock along with most of the other bridge personnel. At almost every station on the Klingon bridge, a body lay slumped over the controls as if they had been killed on duty. A white-ish residue covered the deceased.

"Vhat happened?" Chekov demanded to no one in particular. "How did vat happen?"

"I don't know, but we're going to find out. Chekov, you have the Conn. Sulu, Spock…get Dr. McCoy up here along with five security officers. We're going to get to the bottom of this," Kirk turned to head to the elevator. "meet me in the transportation room."

**XxXxXxXx**

Samus narrowly avoided an ambush. From around the corner came at least five of them…Metroids. Five well-aimed freeze blasts sent them crashing to the ground and five well-aimed missiles took care of them once and for all. She continued down the hall, hoping to come to the bridge soon. An automatic door slid open and she reached her destination.

Dead. Slumped over their control stations as though taken completely by surprise and at once. She had to push one of them out of the way to get at some of the controls.

A ship…nearby?

Samus read the scanner readings again. How did the other ship get here so silently? And if they got aboard this ship…there's no telling what trouble they could get into. They didn't know how to destroy the Metroids.

"Hey, you! Vite there! Identify yourself!"

Samus spun around in alarm to find the viewing screen mounted at the front of the bridge. A face filled it now, one that demanded she answer his questions. Samus lowered the opaque shielding in front of her eyes so he could see that she was human. The look of surprise on his face was genuine.

"I'm Samus Aran," Samus started. "I'm here to eliminate what has destroyed this ship's crew. I advise you not to send anyone over. I can take care of this myself."

"The captain alveady left," The man said. "he should be on ze ship vite now."

"Then he is in danger!" Samus turned, reactivating the shielding to her face, and hurried off the bridge.

"Vait!" The man shouted behind her, but there was no time for waiting. The Captain's life could be in danger.

**XxXxXxXx**

The party materialized in what appeared to be an abandoned room.

"Transporters are inoperative on this end, Captain." Spock said, taking TriCorder readings. "We should have materialized in their transporter room."

"That factor doesn't effect us very much at the moment, Mr. Spock. Let's move out." Kirk gripped the phaser he was holding tightly and glanced out of the automatic door down the hallway. Once he realized it was clear, the party moved out.

"Captain, TriCorder readings are off the chart," Sulu informed. "whatever possesses that amount of power…it's headed for us. Over there!" he pointed in the direction of the power source.

"Phasers on stun." Kirk commanded. The group warily faced down the hallway, waiting for whatever was there to show itself.

Seconds turned to minuets until Sulu said, "Captain…whatever it was…it's gone."

"All right. Doctor, and you three…this way." Kirk motioned for three of the five security officers to come with him and McCoy. "The rest of you, go with Spock. Try to find anything that could solve this mystery of why this crew is dead."

"Understood, Captain," Spock pointed down the hall, and his group began to make their way down it. Kirk and his went the opposite direction.

"Jim…do you have any theories on what could have done this?" McCoy asked.

"No, Bones, as far as we know…we just discovered a whole new race of killing creatures," Kirk's face was grim. "be on guard."

"If possible, I would like to examine one of the corpses. After all, you dragged me out here for that reason, right? I'm a doctor…I'm suppost to stay on the ship unless needed. You know how much I hate that transporter."

"Yes, Bones. I know." Kirk pointed to a small map mounted on the wall. "The bridge is just up ahead."

"Captain!" One of the security officers shouted. "There's someone…or something… heading directly towards us!"

Kirk raised his phaser at the door in front of him, the others doing the same. The door whooshed open and a robot-like figure darted out, weapon raised in place of a right arm. The Enterprise crew didn't move as the robot lowered the weapon and de-activated some sort of screening over its eyes.

Kirk blinked hard. The newcomer wasn't a robot…she was simply someone suited in a specially designed uniform for dealing with the unknown.

"My name is Samus Aran." She said. "I take it you are from the other ship?"

"Yes, we are." Kirk replied.

"You're in danger here." Samus said. "I can deal with the creatures that killed this crew…but you don't have suitable weapons. Return to your ship at once."

"Ms. Aran, we are as qualified to identify this threat and stop it as you are." Kirk interjected.

Samus cast him a glance. "You don't understand. The only thing that can kill Metroids are freeze guns and missiles, two weapons I have at my disposal. Your handheld weapons won't have any effect on them."

"The things that did this to the crew…they're called Metroids?" McCoy asked.

"Yes. They drain you of your power and use it for their own, killing you in the process. They were thought to be extinct…but then they somehow got here." Samus growled.

"We'll have to worry about that later. Right now, I think we should re-unite with the others again," Kirk turned to his crew. "be on guard."

"You can't go alone." Samus said. "I will come with you."

"Then let's go."

**XxXxXxXx**

"Mr. Spock, in there!" Sulu said, pointing with his TriCorder at a nearby door. "Someone's in there…a Klingon!"

Spock knocked loudly. "Can you hear me? I'm First Officer Spock of the starship _Enterprise_. We're here to rescue you."

The door opened slowly to reveal typical Klingon facial features. "How did you survive?" he asked shakily.

"What do you mean?" Spock asked.

"They attacked us…I'm the only one left," The Klingon sighed in loss. "I'm Captain Korr. If I were you I would save myself. Contact your ship and get out of here!"

"But why?" Spock asked.

"Because I can assure you they're planning to destroy you too." Korr stepped nervously out of the room. "We must leave at once!"

"My Captain is still on board," Spock said firmly. "and until we find him and his party we're not leaving."

"Sacrifices must be made!" Korr shouted. "We must evacuate!"

Spock pulled out his communicator. "Spock to Captain."

"Kirk here. What is it, Spock?"

"We'll meet you on the bridge. Captain, we found a survivor."

"All right. Kirk out."

"Spock, look there!" Sulu exclaimed.

Spock wheeled around to see what appeared to be a floating brain with four claws hanging underneath it. The brain-like tissue was surrounded by a clear, jellylike substance, protecting it. Spock pulled his phaser out slowly.

"That's one of them! They killed my crew!" Korr screamed.

**XxXxXxXx**


	2. Chapter 2

**CHAPTER 2**

Spock fired his phaser, but the beam was absorbed into the creature in front of him. It began gliding down the hallway a bit faster, making some sort of screeching noise. Another appeared at the end of the hall.

"Phasers don't work!" Korr shouted, grabbing Spock's arm. "Our only chance is to run!"

One of the security guards turned and took the Klingon's advice, but he didn't get far. The claws on the bottom of the strange alien latched firmly on his head, and the guard's screams were lost in the jelly substance.

"Quickly, while it's distracted!" Korr leapt for the door. The other alien at the end of the hall zipped forward towards the fallen security guard, latching onto his shoulder. The group darted along the halls until another of them appeared.

"We're trapped!" Korr exclaimed as two more came up behind them.

The first once seemed to be deciding who to attack first, its eyeless jellylike brain choosing the closest.

"Mr. Spock!" Sulu shouted in alarm seconds before the alien latched itself onto his superior's head. Before anyone could do anything, a door at the end of the hall opened and a robot ran out, directing its weapon at the Vulcan who had fallen prey to the alien. In one smooth shot, the alien was blasted off his head, hitting the wall and shattering into a million tiny pieces.

Spock sank to the ground, strength gone. Sulu and the others bearing weapons turned the on the robot.

"It's all right, Mr. Sulu, she's with us." Kirk stepped out from around the robot and headed to Spock.

"She, sir?" Sulu asked in confusion.

The robot lowered reflective shielding from its eyes and he found himself staring into the eyes of a young woman.

"This is Samus Aran and she's here to help us stop this threat." Kirk explained. "Apparently these aliens that have taken over this vessel can only be destroyed with weapons like hers."

Samus turned towards Korr. "How did they get aboard your ship in the first place?"

"We beamed up with them…it wasn't until later that we found out they were dangerous." Korr admitted.

McCoy tapped Samus on her shoulder. "If you don't mind, I would like to get a closer look at the dead and the aliens that killed them."

Samus nodded towards were the defeated Metroid lay. "Quickly, though. They know there are still survivors. We'll retreat to the bridge and form a plan there when you are through."

McCoy began analyzing the alien with his TriCorder, his features screwing up in shock.

"What is it, Bones?" Kirk asked.

"Power…they live off of others' power." McCoy said. "They kill to live." No sooner had he said this then two more Metroids rounded the corner at the end of the hall and began drifting towards them.

"I'll meet you at the bridge! Move out!" Samus shouted, firing her weapon at them.

The _Enterprise_ crew along with captain Korr turned and ran, Spock being helped along by Kirk. "Good Lord, Jim! How have we managed to survive this long?" McCoy demanded when the bridge doors slid shut behind them.

"Because the Metroids haven't spread the word yet." Spock said simply. "But very soon we will have more than we can handle on our hands."

"Then why don't we just leave now?" Kirk asked.

"As soon as I've finished my TriCorder readings." McCoy said from over by a dead Klingon by the communications center. "Then we can blow this contaminated ship to the heavens."

"You can't do that!" Korr shouted. "You'll be waging a war on my people by destroying one of our finest battleships!"

"Why are you out here, anyway?" Kirk demanded. "And in a battle cruiser at that. Explain."

Korr opened his mouth and then shut it again, trying to find the right words. "We…were charting these parts of the stars. We didn't know what we would run into and the extra safety precautions could always save lives if the time came."

"I'm not buying it." Kirk glared. "Why are you really out here…and how did Metroids get aboard your ship?"

Korr gave a defeated sigh. "Research. We captured them from a planet and brought them here, planning to examine the life forms. As I'm sure you know, things took a turn for the worst. We wanted to surprise the empire with our findings….but that dream—like my men—has died."

Kirk nodded. "Korr, you know that abandoning your ship now is mandatory. We will eliminate both it and the Metroids once we're all safely onboard the _Enterprise_."

"The shields on this cruiser are too strong to be penetrated by the phasers and torpedoes your ship is armed with. This bird-of-prey will have to be destroyed from the inside. I must stay behind." Korr said fiercely. "Get your female fighter and leave...before something worse happens. Captain… you know I speak the truth. Klingon defenses have grown dramatically."

The _Enterprise_ captain nodded slowly. "I'm guessing you'd rather die on your ship than in custody, like any other captain."

Korr saluted. "I took a vow to," he said clearly.

The bridge doors burst open and Samus ran through, covered in Metroid remains. "We have to get out of here." She said. "Now."

"Doc, you got everything you need?" Kirk asked.

"Let's get the hell out of here, Jim," McCoy responded.

Kirk flipped open his communicator. "Kirk to _Enterprise_! Come in quickly!"

"Yes, sir. Chekov here."

"Beam all but two up. One's staying with the ship and the other's retrieving her shuttlecraft. Open a bay door so she can dock with us."

"Yes, sir. Beaming up."

The doors to the bridge opened again. Before anyone could do anything, a Metroid spotted the group and latched onto Sulu's arm. The sparkle of the transporter surrounded the party and they vanished.

Samus cast a glance at Korr, a serious look on her face. "Get rid of this ship." She commanded before turning and running down the hall towards where her craft was attached to the side of the warship. Korr turned his attention to one of the control panels and set the self-destruct.

Klingonese filled the bridge, translating roughly to English as: "This ship will self destruct in five minuets."

**XxXxXxXx**

The transporter personnel were shocked, to say the least. The strange alien detached itself from Sulu and darted at them, screaming. They dived to the side, in doing so their movement activated the doors behind them and they opened to the hall. The Metroid flew down the corridor, already thinking of its next meal.

"What the hell was that?" one of the men demanded.

"That," Kirk said. "was a Metroid. We, at the moment, can't defeat them ourselves. Our companion we met on the Klingon ship can. She'll be over shortly."

No sooner had he said this than Uhura's voice came over the speakers. "Captain, small craft successfully docked."

"Good. Everyone to your posts. Not a moment to lose now." Kirk began taking long strides to reach the bridge.

Everyone that had beamed over to the Klingon ship began to follow, a couple breaking away from the group at times. The remaining party reached the bridge.

The image of the Klingon vessel was on-screen, and every now and then Kirk caught sight of a flare of fire somewhere on the ship. The self-destruct process had begun. The bridge doors opened and Samus walked in, flanked by two security officers.

"Sir!" one of them said. "The alien! It's here…somewhere in engineering!"

"Captain, permission to seek it out and destroy it?" Samus asked immeadentally.

"Permission granted." Kirk responded.

"Captain, you might want to see this…" Spock stated calmly. Kirk turned towards the viewing screen, the bird-of-prey was giving off a brilliant light show.

In the final finale, a bright fireball engulfed the ship and it was no more; Klingons and Metroids alike destroyed.

Kirk turned away from the screen and pressed a button on the command chair. "Captain to engineering. Everyone evacuate as soon as possible. This is an emergency. All personnel evacuate engineering. This is not a drill." He switched the button off and turned towards Uhura.

"Go to yellow alert."

"Yellow alert, Captain." She said as an alarm began to blare. Kirk turned to Samus.

"I'm coming too, but only to aid my crewmen."

She nodded, and the two of them set out.

**XxXxXxXx**

Two crewmen.

That was how many lay dead just in the entrance of engineering. Kirk's heart sank. Both those men had only been in their early twenties.

At least he could count his blessings. The whole of the engineering crew had otherwise safely evacuated. "Be on guard." Samus warned. "There's no telling where it may be. It may be draining your ship of power or killing another of your men."

Kirk nodded, eyes darting around the room. Nothing out of the ordinary. Samus turned her weapon on him suddenly. "Don't move! It's behind you." She said calmly.

Kirk froze, not moving an inch. Samus' head traced the Metroid's progress until she was staring directly above his head. "Duck!" She hissed.

Kirk ducked and rolled just before the Metroid would have latched itself to the top of his head. Samus fired, freezing the alien in its tracks. A missile finished it—and the horror it had caused—off.

**XxXxXxXx**


	3. Chapter 3

** CHAPTER 3**

"Samus Aran, I award you with this as a symbol of our gratitude towards what you have done for us." Kirk slipped the medal over her head. "The _Enterprise_ crew thanks you."

Samus brushed blonde hair away from her face. Without her Power Suit, she was simply a young girl with extraordinary training to defeat threats. She glanced down at the silver medal, which had two crossed palm leaves on it surrounded by stars. The Starfleet Federation logo was on the back.

"Thank you, sir." She said. "It has been a pleasure working for you."

"Same for me."

"Although, sir, if you don't mind…I need to get back to my ship. I was called off course by readings on my instrument panel that showed Metroids were aboard the Klingon ship."

"By all means, go." Kirk motioned in the direction to take to get back to the shuttle docking.

** XxXxXxXx**

"Can you believe after all that…and we didn't even complete a fraction of our mission?" Kirk asked, watching as Samus' small orange craft darted away into the void of space.

"It would have been impossible to." Spock stated.

"Then we'll just have to work twice as hard now." Kirk smiled. "Sulu, full speed ahead. Let's see if we can chart some interesting planets ahead."

"Full speed, Captain." Sulu reported.

_** Space, the Final Frontier.**_

_** These are the voyages of the starship Enterprise.**_

_** Its five year mission:**_

_** To explore strange new worlds**_

_** To seek out new life, and new civilization**_

_** To boldly go where no man has gone before.**_

__**XxXxXxXx**

** HOORAY! Star Trek/ Metroid Fic completed! This was actually pretty hard to do; I ended up writing the whole story in Biology in my free time and then typing it up. Took a total of about two weeks. Looking back at the paper and then at the computer takes a long time.**

** 19 pages of notebook paper! That's how much this story took up! From beginning to end! Wow! I could have made 19 ninja stars!**

** Ok, enough of that. No Flames! REMEMBER TO REVIEW!**

** Hasta la Vista, Readers!**

** Lordoftheghostking28**


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